[English] 日本語
Yorodumi
- EMDB-34475: Cryo-EM structure of the full transcription activation complex Nt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34475
TitleCryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC
Map data
Sample
  • Complex: full transcription activation complex with two activators NtcA and NtcB
    • DNA: DNA (125-MER)
    • DNA: DNA (125-MER)
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit gamma
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: NtcB
    • Protein or peptide: NtcA
Keywordstranscription activation complex / coordinated regulation / TRANSCRIPTION
Function / homology
Function and homology information


sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / magnesium ion binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-binding transcription factor activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
: / RNA polymerase sigma factor, RpoD-like, cyanobacteria / Transcription regulator, NtcA / DNA-directed RNA polymerase, subunit gamma / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / : / helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. ...: / RNA polymerase sigma factor, RpoD-like, cyanobacteria / Transcription regulator, NtcA / DNA-directed RNA polymerase, subunit gamma / DNA-directed RNA polymerase subunit RpoC1 / DNA-directed RNA polymerase, subunit beta'' / : / helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RmlC-like jelly roll fold / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Global nitrogen regulator / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit gamma / DNA-directed RNA polymerase subunit beta' / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha / Nitrogen assimilation transcriptional activator
Similarity search - Component
Biological speciesAnabaena (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsHan SJ / Jiang YL / You LL / Shen LQ / Wu XX / Yang F / Kong WW / Chen ZP / Zhang Y / Zhou CZ
Funding support China, 4 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37020301, XDA24020302 China
National Natural Science Foundation of China (NSFC)32171198 China
Ministry of Science and Technology (MoST, China)2018YFA090070 China
Chinese Academy of Sciences2020452 China
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: DNA looping mediates cooperative transcription activation.
Authors: Shu-Jing Han / Yong-Liang Jiang / Lin-Lin You / Li-Qiang Shen / Xiaoxian Wu / Feng Yang / Ning Cui / Wen-Wen Kong / Hui Sun / Ke Zhou / Hui-Chao Meng / Zhi-Peng Chen / Yuxing Chen / Yu Zhang / Cong-Zhao Zhou /
Abstract: Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here ...Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria.
History
DepositionOct 9, 2022-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_34475.png

Downloads & links

-
Map

FileDownload / File: emd_34475.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 350 pix.
= 374.5 Å		1.07 Å/pix.
x 350 pix.
= 374.5 Å		1.07 Å/pix.
x 350 pix.
= 374.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.5262536 - 2.3371446
Average (Standard dev.)0.0065378887 (±0.055032834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 374.50003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_34475_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34475_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : full transcription activation complex with two activators NtcA an...

EntireName: full transcription activation complex with two activators NtcA and NtcB
Components
  • Complex: full transcription activation complex with two activators NtcA and NtcB
    • DNA: DNA (125-MER)
    • DNA: DNA (125-MER)
    • Protein or peptide: DNA-directed RNA polymerase subunit beta
    • Protein or peptide: DNA-directed RNA polymerase subunit beta'
    • Protein or peptide: DNA-directed RNA polymerase subunit alpha
    • Protein or peptide: DNA-directed RNA polymerase subunit gamma
    • Protein or peptide: DNA-directed RNA polymerase subunit omega
    • Protein or peptide: RNA polymerase sigma factor SigA
    • Protein or peptide: NtcB
    • Protein or peptide: NtcA

+
Supramolecule #1: full transcription activation complex with two activators NtcA an...

SupramoleculeName: full transcription activation complex with two activators NtcA and NtcB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC. 7120
Molecular weightTheoretical: 718 KDa

+
Macromolecule #1: DNA (125-MER)

MacromoleculeName: DNA (125-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Anabaena (bacteria)
Molecular weightTheoretical: 38.723902 KDa
SequenceString: (DG)(DT)(DT)(DA)(DA)(DG)(DT)(DG)(DT)(DA) (DA)(DT)(DG)(DC)(DA)(DA)(DA)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DT)(DA)(DT)(DT)(DC) (DT)(DC)(DT)(DA)(DT)(DG)(DC)(DA)(DA)(DA) (DA) (DA)(DA)(DC)(DG)(DC)(DA) ...String:
(DG)(DT)(DT)(DA)(DA)(DG)(DT)(DG)(DT)(DA) (DA)(DT)(DG)(DC)(DA)(DA)(DA)(DA)(DA)(DA) (DC)(DG)(DC)(DA)(DT)(DA)(DT)(DT)(DC) (DT)(DC)(DT)(DA)(DT)(DG)(DC)(DA)(DA)(DA) (DA) (DA)(DA)(DC)(DG)(DC)(DA)(DT)(DT) (DA)(DA)(DT)(DA)(DC)(DG)(DA)(DG)(DA)(DA) (DT)(DT) (DT)(DT)(DG)(DT)(DA)(DG)(DC) (DT)(DA)(DC)(DT)(DT)(DA)(DT)(DA)(DC)(DA) (DA)(DA)(DA) (DT)(DT)(DC)(DA)(DG)(DG) (DA)(DA)(DA)(DA)(DT)(DT)(DT)(DT)(DT)(DC) (DT)(DG)(DT)(DA) (DT)(DA)(DA)(DT)(DG) (DG)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DA) (DC)(DG)(DG)(DA)(DT) (DG)(DC)(DA)(DG) (DG)

+
Macromolecule #2: DNA (125-MER)

MacromoleculeName: DNA (125-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Anabaena (bacteria)
Molecular weightTheoretical: 38.571723 KDa
SequenceString: (DC)(DC)(DT)(DG)(DC)(DA)(DT)(DC)(DC)(DG) (DT)(DG)(DA)(DG)(DT)(DC)(DG)(DA)(DG)(DG) (DG)(DT)(DA)(DA)(DT)(DA)(DA)(DC)(DA) (DG)(DA)(DA)(DA)(DA)(DA)(DT)(DT)(DT)(DT) (DC) (DC)(DT)(DG)(DA)(DA)(DT) ...String:
(DC)(DC)(DT)(DG)(DC)(DA)(DT)(DC)(DC)(DG) (DT)(DG)(DA)(DG)(DT)(DC)(DG)(DA)(DG)(DG) (DG)(DT)(DA)(DA)(DT)(DA)(DA)(DC)(DA) (DG)(DA)(DA)(DA)(DA)(DA)(DT)(DT)(DT)(DT) (DC) (DC)(DT)(DG)(DA)(DA)(DT)(DT)(DT) (DT)(DG)(DT)(DA)(DT)(DA)(DA)(DG)(DT)(DA) (DG)(DC) (DT)(DA)(DC)(DA)(DA)(DA)(DA) (DT)(DT)(DC)(DT)(DC)(DG)(DT)(DA)(DT)(DT) (DA)(DA)(DT) (DG)(DC)(DG)(DT)(DT)(DT) (DT)(DT)(DT)(DG)(DC)(DA)(DT)(DA)(DG)(DA) (DG)(DA)(DA)(DT) (DA)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DG)(DC)(DA)(DT) (DT)(DA)(DC)(DA)(DC) (DT)(DT)(DA)(DA) (DC)

+
Macromolecule #3: DNA-directed RNA polymerase subunit beta

MacromoleculeName: DNA-directed RNA polymerase subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 126.781531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVSSKKFNQV DKGRGMISEN YIEPAFLLPD LIEIQRSSFR WFLEEGLIEE LNSFSPITDY TGKLELHFLG HNYKLKEPKY SVEEAKRRD STYAVQMYVP TRLLNKETGD IKEQEVFIGD LPLMTDRGTF IINGAERVIV NQIVRSPGVY YKSEIDKNGR R TYSASLIP ...String:
MVSSKKFNQV DKGRGMISEN YIEPAFLLPD LIEIQRSSFR WFLEEGLIEE LNSFSPITDY TGKLELHFLG HNYKLKEPKY SVEEAKRRD STYAVQMYVP TRLLNKETGD IKEQEVFIGD LPLMTDRGTF IINGAERVIV NQIVRSPGVY YKSEIDKNGR R TYSASLIP NRGAWLKFET DRNDLVWVRI DKTRKLSAQV LLKALGLSDN EIFDALRHPE YFQKTIEKEG QFSEEEALME LY RKLRPGE PPTVLGGQQL LDSRFFDPKR YDLGRVGRYK LNKKLRLSVP DTVRVLTSGD ILAAVDYLIN LEYDIGSIDD IDH LGNRRV RSVGELLQNQ VRVGLNRLER IIRERMTVSD AEVLTPASLV NPKPLVAAIK EFFGSSQLSQ FMDQTNPLAE LTHK RRLSA LGPGGLTRER AGFAVRDIHP SHYGRICPIE TPEGPNAGLI GSLATHARVN QYGFLETPFR PVENGRVRFD QPAAY MTAD EEDDLRVAPG DIPVDENGYI IGPQVPVRYR QEFSTTTPEQ VDYVAVSPVQ IVSVATSMIP FLEHDDANRA LMGSNM QRQ AVPLLKPERP LVGTGLEAQG ARDSGMVIVS RTDGDVVYVD ATEIRVRVSG QLPTASGKST DNGQLTSQKG QEIRYTV SK YQRSNQDTCL NQKPLVRIGE RVVAGQVLAD GSSTEGGELA LGQNIVVAYM PWEGYNYEDA ILISERLVQD DIYTSIHI E KYEIEARQTK LGPEEITREI PNVGEDALRQ LDEQGIIRIG AWVEAGDILV GKVTPKGESD QPPEEKLLRA IFGEKARDV RDNSLRVPNG EKGRVVDVRL FTREQGDELP PGANMVVRVY VAQKRKIQVG DKMAGRHGNK GIISRILPIE DMPYLPDGSP VDIVLNPLG VPSRMNVGQV FECLLGWAGH TLGVRFKITP FDEMYGEESS RRIVHGKLQE ARDETGKDWV YNPDDPGKIM V YDGRTGEA FDRPVTIGVA YMLKLVHLVD DKIHARSTGP YSLVTQQPLG GKAQQGGQRF GEMEVWALEA FGAAYTLQEL LT VKSDDMQ GRNEALNAIV KGKAIPRPGT PESFKVLMRE LQSLGLDIAV HKVETQADGS SLDVEVDLMA DQLARRTPPR PTY ESLSRE SLDDDE

UniProtKB: DNA-directed RNA polymerase subunit beta

+
Macromolecule #4: DNA-directed RNA polymerase subunit beta'

MacromoleculeName: DNA-directed RNA polymerase subunit beta' / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 147.137484 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIFRNRVVDK GQLRNLISWA FTHYGTARTA VMADKLKDLG FRYATRAGVS ISVDDLMVPP SKRSLLEAAE EEIRATEVRY QRGEITEVE RFQKVIDTWN GTSEALKDEV VTHFKQTNPL NSVYMMAFSG ARGNISQVRQ LVGMRGLMAD PQGEIIDLPI K TNFREGLT ...String:
MIFRNRVVDK GQLRNLISWA FTHYGTARTA VMADKLKDLG FRYATRAGVS ISVDDLMVPP SKRSLLEAAE EEIRATEVRY QRGEITEVE RFQKVIDTWN GTSEALKDEV VTHFKQTNPL NSVYMMAFSG ARGNISQVRQ LVGMRGLMAD PQGEIIDLPI K TNFREGLT VTEYIISSYG ARKGLVDTAL RTADSGYLTR RLVDVSQDVI IREIDCGTTR GIPVRPMTEG SKTLIKLSTR LL GRVVGED VIHPKTKEVI APRNTPISDD LAKEIEKAGV AEVVVRSPLT CEAARSVCQH CYGWSLAHAK MVDLGEAVGI IAA QSIGEP GTQLTMRTFH TGGVFTGEVA QQVRSKMDGT IKLPRKLRTR THRTRHGEDA LFVESNGIMI LEPRKEGSET PAPQ EIHVT QGSTIYIVDG QQVKKGQLLA EVALGGRTTR TNTEKAVKDV ASDLAGEVKF AEVVPEQKTD RQGNTTTTAA RGGLI WILS GEVYNLPPGA ELVVKNGDRV ETNGVLAETK LTTIHGGVVR LPEATPGKST REIEIITASV VLDQATVTVQ SSQGRN NYL ITTGNNQVFN LRATPGTKVQ NGQVVAELID DRYRTTTGGF LKFAGVEVQK KGKAKLGYEV VQGGTLLWIP EETHEVN KD ISLLLVEDGQ YVEAGTEVVK DIFCQNSGVV EVTQKNDILR EVVVKPGELL MVDDPEAVIG RDNTLLQPGE ELLGQVAT E LRYIQYVESP EGPALLSRPV VEFAVPSNPD VPSTTSVSQQ TGRSIQMRAV QRLPYKDSER VKSVEGVELL RTQLVLEIE QEGEQEHNAS PLAADIELIP DLEDADVQRL QLVILESLVL RRDIAADATQ GSTQTSLEVK DGDTIVPGSV VARTQILSKE GGIVRGVQK GSEAVRRCLV LRHSDMATLN ISAKPKVKAG DLIVAGTELA PGIFAEESGQ IVGVKNAGES TTTQDAALST Q NYAVTIRA GRPYRVSPGA VLQIEDGDLV QRGDNLVLLV FERAKTGDII QGLPRIEELL EARKPKEACI LAKRGGEVKV VY GDGDEAI AIKVIESNGV VTDYPLGPGQ NLAMPDGSVV PAGQPLSDGP SNPHEILEVF FSLGSEDGVY ACASHALQKV QTF LVNEVQ MVYQSQGIDI ADKHIEVIVR QMTNKVRIDD GGDTTMLPGE LVELRQVEQV NEAMAITGGA RAQYTPVLLG ITKA SLNTD SFISAASFQE TTRVLTEAAI EGKSDWLRGL KENVIIGRLI PAGTGYNTYD EPGMLEDYST LETTSVLDET DDPLD MVLD DRTARAYNLD SPGLAETGFN NRRSILDDDE LIADEIHDLV EAEVEVDDEV DDDYEDDDED DDDYED

UniProtKB: DNA-directed RNA polymerase subunit beta'

+
Macromolecule #5: DNA-directed RNA polymerase subunit alpha

MacromoleculeName: DNA-directed RNA polymerase subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 26.166613 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVAQFQIECV ESNTEESRNH YSKFILEPLE RGQGTTVGNA LRRVLLSNLE GTAVTAVRIA GVSHEFATVP GVREDVLEII MRMKEVILK SYSSQAQIGR LLVNGPTTIT ASHFDLPSEV EVIDPTQYVA TIAEGGKLEM EFRIERGKGY RTVERGREEA T SLDFLQID ...String:
MVAQFQIECV ESNTEESRNH YSKFILEPLE RGQGTTVGNA LRRVLLSNLE GTAVTAVRIA GVSHEFATVP GVREDVLEII MRMKEVILK SYSSQAQIGR LLVNGPTTIT ASHFDLPSEV EVIDPTQYVA TIAEGGKLEM EFRIERGKGY RTVERGREEA T SLDFLQID SIFMPVRKVN YSVEEVRADG SIPKDRLLLE VWTNGSISPQ EALSSAAGIL VDLFNPLKDI SLEPTDTN

UniProtKB: DNA-directed RNA polymerase subunit alpha

+
Macromolecule #6: DNA-directed RNA polymerase subunit gamma

MacromoleculeName: DNA-directed RNA polymerase subunit gamma / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 70.653055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRPAQTNQFD YVKIGLASPE RIRQWGERTL PNGQVVGEVT KPETINYRTL KPEMDGLFCE RIFGPAKDWE CHCGKYKRVR HRGIVCERC GVEVTESRVR RHRMGYIKLA APVAHVWYLK GIPSYISILL DMPLRDVEQI VYFNSYVVLS PGNAETLTYK Q LLSEDQWL ...String:
MRPAQTNQFD YVKIGLASPE RIRQWGERTL PNGQVVGEVT KPETINYRTL KPEMDGLFCE RIFGPAKDWE CHCGKYKRVR HRGIVCERC GVEVTESRVR RHRMGYIKLA APVAHVWYLK GIPSYISILL DMPLRDVEQI VYFNSYVVLS PGNAETLTYK Q LLSEDQWL EIEDQIYSED SQLQGVEVGI GAEALLRLLA DINLEQEAES LREEIGSAKG QKRAKLIKRL RVIDNFIATG SK PEWMVMT VIPVIPPDLR PMVQLDGGRF ATSDLNDLYR RVINRNNRLA RLQEILAPEI IVRNEKRMLQ EAVDALIDNG RRG RTVVGA NNRPLKSLSD IIEGKQGRFR QNLLGKRVDY SGRSVIVVGP KLKIHQCGLP REMAIELFQP FVINRLIRSG MVNN IKAAK KLISRNDPSV WDVLEEVIEG HPVMLNRAPT LHRLGIQAFE PILVEGRAIQ LHPLVCPAFN ADFDGDQMAV HVPLS LESQ AEARLLMLAS NNILSPATGR PIITPSQDMV LGAYYLTAEN PGATKGAGKY FASLDDVIMA FQQEQIDLHA YVYVRF DGD VESDQPDTEP VKVTTNEDGS RTVLYKYRRV REDAQGNVIS QYIYTTPGRV IYNKAIQEAL AS

UniProtKB: DNA-directed RNA polymerase subunit gamma

+
Macromolecule #7: DNA-directed RNA polymerase subunit omega

MacromoleculeName: DNA-directed RNA polymerase subunit omega / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed RNA polymerase
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 9.14349 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLKRSKFETT QSQIMHRAED LISAASNRYR ITVQVANRAK RRRYEEFESA EDAMMKPVLR AIIEMSDELT QPEIIGEI

UniProtKB: DNA-directed RNA polymerase subunit omega

+
Macromolecule #8: RNA polymerase sigma factor SigA

MacromoleculeName: RNA polymerase sigma factor SigA / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 45.717027 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNQANNVLDS IYQPDLEIMN QPEIELDDLL IEEDEDLLLA DDGDIDEFLE PQTDEDDAKS GKAAKSRRRT QSKKKHYTED SIRLYLQEI GRIRLLRADE EIELARKIAD LLELERVRER LSEKLERDPR DSEWAEAVQL PLPAFRYRLH IGRRAKDKMV Q SNLRLVVS ...String:
MNQANNVLDS IYQPDLEIMN QPEIELDDLL IEEDEDLLLA DDGDIDEFLE PQTDEDDAKS GKAAKSRRRT QSKKKHYTED SIRLYLQEI GRIRLLRADE EIELARKIAD LLELERVRER LSEKLERDPR DSEWAEAVQL PLPAFRYRLH IGRRAKDKMV Q SNLRLVVS IAKKYMNRGL SFQDLIQEGS LGLIRAAEKF DHEKGYKFST YATWWIRQAI TRAIADQSRT IRLPVHLYET IS RIKKTTK LLSQEMGRKP TEEEIATRME MTIEKLRFIA KSAQLPISLE TPIGKEEDSR LGDFIESDGE TPEDQVSKNL LRE DLEKVL DSLSPRERDV LRLRYGLDDG RMKTLEEIGQ IFNVTRERIR QIEAKALRKL RHPNRNSVLK EYIR

UniProtKB: RNA polymerase sigma factor SigA

+
Macromolecule #9: NtcB

MacromoleculeName: NtcB / type: protein_or_peptide / ID: 9 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 34.941363 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLEQLQAFL AIAETGSFQK AASKCGVTQS TISRQIQSLE ADLGLELFHR TNHSKLTLGG ERLLPRARKI CLEWETATQE LGDLIAGKQ PELCIAAIHS LCGSYLPPVL QKFCRDYPEV QLRVTSLGSD RALKVLKDGL VDLAIVMNNR FLTTGRDMVV E VLYDEPIE ...String:
MRLEQLQAFL AIAETGSFQK AASKCGVTQS TISRQIQSLE ADLGLELFHR TNHSKLTLGG ERLLPRARKI CLEWETATQE LGDLIAGKQ PELCIAAIHS LCGSYLPPVL QKFCRDYPEV QLRVTSLGSD RALKVLKDGL VDLAIVMNNR FLTTGRDMVV E VLYDEPIE LLTAANHPLA AYERVPWSEL VRYPQVVFKD GYGMQRLVQE KFERLEATLQ AALEVNTLDA FRGVVRQGEL IA LLPSSAL VEARLDPTLA VRPLANSALP ENSGLTRRVV MVTTQDRLQI PPIKHFWQLV RENIPPIVER QRSAS

UniProtKB: Nitrogen assimilation transcriptional activator

+
Macromolecule #10: NtcA

MacromoleculeName: NtcA / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Anabaena (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576
Molecular weightTheoretical: 24.951266 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIVTQDKALA NVFRQMATGA FPPVVETFER NKTIFFPGDP AERVYFLLKG AVKLSRVYEA GEEITVALLR ENSVFGVLSL LTGNKSDRF YHAVAFTPVE LLSAPIEQVE QALKENPELS MLMLRGLSSR ILQTEMMIET LAHRDMGSRL VSFLLILCRD F GVPCADGI ...String:
MIVTQDKALA NVFRQMATGA FPPVVETFER NKTIFFPGDP AERVYFLLKG AVKLSRVYEA GEEITVALLR ENSVFGVLSL LTGNKSDRF YHAVAFTPVE LLSAPIEQVE QALKENPELS MLMLRGLSSR ILQTEMMIET LAHRDMGSRL VSFLLILCRD F GVPCADGI TIDLKLSHQA IAEAIGSTRV TVTRLLGDLR EKKMISIHKK KITVHKPVTL SRQFT

UniProtKB: Global nitrogen regulator

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration17 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMKClpotassium chloride
5.0 mMMgCl2magnesium chloride
10.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
2.0 mMDTTDithiothreitol

Details: 10 mM HEPES pH 7.5, 100 mM KCl, 5 mM MgCl2 and 2 mM DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I
DetailsThis sample was

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5047 / Average electron dose: 50.0 e/Å2
Details: Images were collected in movie-mode at 40 frames per second.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 566246
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8gzg

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 65446
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8h3v:
Cryo-EM structure of the full transcription activation complex NtcA-NtcB-TAC

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more